Because common_startup is executed and not sourced, this block needs to remain in run.sh

run.sh

@@ -60,6 +60,16 @@ done
 
 ./scripts/common_startup.sh $common_startup_args || exit 1
 
+# If there is a .venv/ directory, assume it contains a virtualenv that we
+# should run this instance in.
+GALAXY_VIRTUAL_ENV="${GALAXY_VIRTUAL_ENV:-.venv}"
+if [ -d "$GALAXY_VIRTUAL_ENV" -a -z "$skip_venv" ];
+then
+    [ -n "$PYTHONPATH" ] && { echo 'Unsetting $PYTHONPATH'; unset PYTHONPATH; }
+    echo "Activating virtualenv at $GALAXY_VIRTUAL_ENV"
+    . "$GALAXY_VIRTUAL_ENV/bin/activate"
+fi
+
 # If you are using --skip-venv we assume you know what you are doing but warn
 # in case you don't.
 [ -n "$PYTHONPATH" ] && echo 'WARNING: $PYTHONPATH is set, this can cause problems importing Galaxy dependencies'